With the function:
overlaps.anno <- annotatePeakInBatch(overlaps, AnnotationData=annoData, output="nearestBiDirectionalPromoters",bindingRegion=c(-2000, 500))
got this warning message:
Annotate peaks by annoPeaks, see ?annoPeaks for details. maxgap will be ignored. Warning messages: 1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequences GL000199.1 and chrM. Note that only ranges located on a non-circular sequence whose length is not NA can be considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information.
What are the out-of-bound ranges? Is it advisable that we get rid of them?